Jens Lagergren <jensl@nada.kth.se> Telephone: +46 8 55 37 85 70, fax: +46 8 55 37 82 14 Address: KTH, Albanova, SBC, S - 100 44 Stockholm Visiting address: Albanova, Roslagstullsbacken 35 (see directions and map) (Denna sida finns ej tillgänglig på svenska.)

Affiliation

I am professor in computer science and computational biology in CB (the Computational Biology department) of CSC. I also belong to SBC (Stockholm Bioinformatics Center). SBC is a joint venture between KTH (Kunliga Tekniska Högskolan, i.e., The Royal Institute of Technology) and SU (Stockholm University). SBC was initially funded by the Swedish Foundation for Strategic Research. Fortunately, CB and SBC are are currently located in the same building. For directions see directions and map to SBC..

Current Courses

• During the spring semester 2010, I will give the course Omics Data and Systems Biologyseminar course .
• During the spring semester 2010, I will also give the course Algorithmic Bioinformatics
• I have somewhat tentative plans to give a course on Bayesian Network during fall 2009.

Research Group

• Computational Biology and Bioinformatics

Ph.D. Students

• Hossein Farahani
• Joel Sjöstrand
• Ali Tofigh

Former Post-docs

• Ann-Charlotte Berglund
• Öjvind Johansson

Former Ph.D. Students

• Lars Arvestad
• Lars Ivansson
• Isaac Elias
• Örjan Svensson

Recent Service

Co-chair program committee WABI 2008

Program committee RECOMB 2008

Program committee ISMB 2007

Program committee WABI 2007.

Program committee RECOMB 2007

Program committee ISMB 2006

Program committee WABI 2006.

Chair program committee Bioinformatics 2006.

Co-organizer Bertinoro Computational Biology Workshop 2006

Program committee CompBioNets 2005

Program committee 3rd RECOMB Satellite Workshop on Comparative Genomics, 2005

Program committee WABI 2005.

Program committee ISMB 2005

Member of the BICI Scientific Advisory Board

Chair program committee Second RECOMB Satellite Workshop on Comparative Genomics, 2004.

Co-organizer Second RECOMB Satellite Workshop on Comparative Genomics, 2004.

Program committee Bioinformatics 2005.

Program committee WABI 2004

Program committee RECOMB 2004

Board member of SocBiN -- Society for Bioinformatics in the Nordic countries.

Refereed Publications since 2000 (in most cases authors are listed in alphabetic order, i.e. computer science style)

Motif Yggdrasil: Sampling from a Tree Mixture Model.

Samuel A. Andersson and Jens Lagergren.

In Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2006), pages 458-472.

Genome-wide survey for biologically functional pseudogenes.

Ö.P. Svensson, L. Arvestad, J. Lagergren

PLoS Computational Biology Vol. 2, No. 5, e46 DOI: 10.1371/journal.pcbi.0020046

New Probabilistic Network Models and Algorithms for Oncogenesis.

M. Hjelm, M. Höglund, and J. Lagergren.

Journal of Computational Biology, May 2006, Vol. 13, No. 4: 853-865.

Compatibility of unrooted phylogenetic trees is FPT.

D. Bryant and J. Lagergren.

Theoretical Computer Science 351 (2006) 296-302

Fast Neighbor Joining.

I. Elias and J. Lagergren.

ICALP 2005, pages 1263--1274

Algorithms for RH Mapping: New Ideas and Improved Analysis.

L. Ivansson and J. Lagergren.

SIAM Journal on Computing 34(1):89--108 (2005)

MSCAN: identification of functional clusters of transcription factor binding sites.

W. Alkema, Öjvind Johansson, Jens Lagergren, and Wyeth W. Wasserman

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W195-8.

PDF

Ancestral Maximum Likelihood of Phylogenetic Trees is Hard

L. Addario-Berry, B. Chor, M. Hallett, J. Lagergren, A. Panconesi, and T. Wareham.

Journal of Bioinformatics and Computational Biology, January 2004, 12:55

doi:10.1142/S0219720004000557

Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution

Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, and Bengt Sennblad

RECOMB 2004, 326-335.

PS

Simultaneous Identification of Duplications and Lateral Transfers

M. Hallett, J. Lagergren, and A. Tofigh

RECOMB 2004, 347-356.

PDF, PS

Ancestral Maximum Likelihood of Phylogenetic Trees is Hard

Louigi Addario-Berry, Benny Chor, Mike Hallett, Jens Lagergren, Alessandro Panconesi, and Todd Wareham

WABI 2003: 202-215

PS A4, PS Letter

Fitting Point on the Real Line and its Application to RH Mapping

J. Håstad, L. Ivansson, and J. Lagergren

J. Algorithms 49(1): 42-62 (2003)

PDF

A polynomial-time algorithm for near-perfect phylogeny

D. Fernandez-Baca, J. Lagergren

SIAM Journal on Computing 32(5): 1115-1127 (2003)

PDF

Bayesian Gene/Species Tree Reconciliation and Orthology Analysis Using MCMC

L. Arvestad, A.C. Berglund, J. Lagergren, and B. Sennblad

Bioinformatics (ISMB) 2003: 7-15

PDF

Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm

Öjvind Johansson, W. Alkema, Wyeth W. Wasserman, and Jens Lagergren

Bioinformatics (ISMB) 2003: 169-176

PS PDF

Towards Identifying Lateral Gene Transfer Events

L. Addario-Berry, M. Hallett, J. Lagergren

Pacific Symposium on Biocomputing 2003: 279-290

PDF

Combining Polynomial Running Time and Fast Convergence for the Disk-Covering Method

J. Lagergren.

Journal of Computer and System Science, 65(3): 481-493 (2002)

Efficient Algorithms for Lateral Gene Transfer Problems.

M.T. Hallett and J. Lagergren.

In RECOMB´01, pages 149-156.

Hunting for Functionally Analogous Genes.

M.T. Hallett and J.Lagergren.

In FSTTCS´00.

New algorithms for the duplication-loss model.

M.T. Hallett and J.Lagergren.

In RECOMB´00, pages 138-146.

PDF

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